Using siRNA for gene silencing is a rapidly evolving tool in molecular biology. There are several methods for preparing siRNA, such as chemical synthesis, in vitro transcription, siRNA expression vectors, and PCR expression cassettes. Irrespective of which method one uses, the first step in designing a siRNA is to choose the siRNA target site. The guidelines below for choosing siRNA target sites are based on both the current literature, and on empirical observations by scientists at Ambion. Using these guidelines, approximay half of all siRNAs yield >50% reduction in target mRNA levels.

For the Best Results, Let Us Design Your sirnas

Ambion has recently partnered with Cenix Bioscience, a leader in the field of RNAi. Cenix has developed a proprietary siRNA design algorithm that yields a much higher percentage of effective siRNAs when compared to siRNAs designed using the rules outlined below. For information on that algorithm, see Designing a Better siRNA. You can order chemically synthesized siRNAs pre-designed using the Cenix algorithm from Ambion. Designs are currently available for >98% of the human, mouse, and rat genes in the RefSeq database. See the Pre-designed siRNA Catalog page for more information. In addition, Ambion offers Silencer Validated siRNAs to a number of important human genes. These siRNAs have actually been tested and verified to reduce target mRNA levels >70%.

General Design Guidelines

If you prefer to design your own siRNAs, you can choose siRNA target sites in a variety of different organisms based on the following guidelines. Corresponding siRNAs can then be chemically synthesized, created by in vitro transcription, or expressed from a vector or PCR product.

1. Find 21 nt sequences in the target mRNA that begin with an AA dinucleotide.

Beginning with the AUG start codon of your transcript, scan for AA dinucleotide sequences. Record each AA and the 3" adjacent 19 nucleotides as potential siRNA target sites. 

This strategy for choosing siRNA target sites is based on the observation by Elbashir et al. (1) that siRNAs with 3" overhanging UU dinucleotides are the most effective. This is also compatible with using RNA pol III to transcribe hairpin siRNAs because RNA pol III terminates transcription at 4-6 nucleotide poly(T) tracts creating RNA molecules with a short poly(U) tail. 

In Elbashir"s and subsequent publications, siRNAs with other 3" terminal dinucleotide overhangs have been shown to effectively induce RNAi. If desired, you may modify this target site selection strategy to design siRNAs with other dinucleotide overhangs, but it is recommended that you avoid G residues in the overhang because of the potential for the siRNA to be cleaved by RNase at single-stranded G residues.

2. Select 2-4 target sequences.

Research at Ambion has found that typically more than half of randomly designed siRNAs provide at least a 50% reduction in target mRNA levels and approximay 1 of 4 siRNAs provide a 75-95% reduction. Choose target sites from among the sequences identified in Step 1 based on the following guidelines:

Ambion researchers find that siRNAs with 30-50% GC content are more active than those with a higher G/C content.
Since a 4-6 nucleotide poly(T) tract acts as a termination signal for RNA pol III, avoid stretches of > 4 T"s or A"s in the target sequence when designing sequences to be expressed from an RNA pol III promoter.
Since some regions of mRNA may be either highly structured or bound by regulatory proteins, we generally select siRNA target sites at different positions along the length of the gene sequence. We have not seen any correlation between the position of target sites on the mRNA and siRNA potency.
Compare the potential target sites to the appropriate genome database (human, mouse, rat, etc.) and eliminate from consideration any target sequences with more than 16-17 contiguous base pairs of homology to other coding sequences. We suggest using BLAST, which can be found on the NCBI server at: 
www.ncbi.nlm.nih.gov/BLAST.
3. Design appropriate controls.

A complete siRNA experiment should include a number of controls to ensure the validity of the data. The editors of Nature Cell Biology have recommended several controls (2). Two of these controls are:

A negative control siRNA with the same nucleotide composition as your siRNA but which lacks significant sequence homology to the genome. To design a negative control siRNA, scramble the nucleotide sequence of the gene-specific siRNA and conduct a search to make sure it lacks homology to any other gene.
Additional siRNA sequences targeting the same mRNA. Perhaps the best way to ensure confidence in RNAi data is to perform experiments, using a single siRNA at a time, with two or more different siRNAs targeting the same gene. Prior to these experiments, each siRNA should be tested to ensure that it reduces target gene expression by comparable levels.